Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments

Journal of Molecular Graphics and Modelling

Volumn 41, Issue , 2013, Pages 20-30

  Karaboga, Arnaud S ^a   Petronin, Florent ^a   Marchetti, Gino ^a   Souchet, Michel ^b   Maigret, Bernard ^a  

^a LORIA   (France)

^b Harmonic Pharma   (France)

Author keywords

3D description; Ligand centric pharmacophoric description; Molecular similarity; Retrospective shape based screening; Spherical harmonic molecular representation

Indexed keywords

3D DESCRIPTION; LIGAND-CENTRIC PHARMACOPHORIC DESCRIPTION; MOLECULAR REPRESENTATIONS; MOLECULAR SIMILARITY; SHAPE BASED;

BIOACTIVITY; CHEMICAL ENGINEERING; HARMONIC ANALYSIS; LIGANDS; THREE DIMENSIONAL COMPUTER GRAPHICS;

THREE DIMENSIONAL;

AREA UNDER THE CURVE; ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; HARMONIC PHARMA CHEMISTRY COEFFICIENT; METRIC SYSTEM; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN TARGETING; QUALITY CONTROL; RECEIVER OPERATING CHARACTERISTIC; VIRTUAL REALITY;

AREA UNDER CURVE; BENCHMARKING; DATABASES, PROTEIN; HUMANS; LIGANDS; MOLECULAR CONFORMATION; PROTEINS; SMALL MOLECULE LIBRARIES; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84874449946     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.01.003     Document Type: Article

References (73)

1. Y.T. Tang, and G.R. Marshall Virtual screening for lead discovery Methods in Molecular Biology 716 2011 1 22
2. A.L. Liu, and G.H. Du Research progress of virtual screening aided drug discovery Yao Xue Xue Bao 44 2009 566 570
3. Y.C. Martin, J.L. Kofron, and L.M. Traphagen Do structurally similar molecules have similar biological activity? Journal of Medicinal Chemistry 45 2002 4350 4358
4. H. Eckert, and J. Bajorath Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches Drug Discovery Today 12 2007 225 233
5. C.G. Wermuth Similarity in drugs: reflections on analogue design Drug Discovery Today 11 2006 348 354
6. A.G. Maldonado, J.P. Doucet, M. Petitjean, and B.T. Fan Molecular similarity and diversity in chemoinformatics: from theory to applications Molecular Diversity 10 2006 39 79
7. J. Auer, and J. Bajorath Molecular similarity concepts and search calculations Methods in Molecular Biology 453 2008 327 347
8. P. Willett Similarity searching using 2D structural fingerprints Methods in Molecular Biology 672 2010 133 158
9. E.J. Gardiner, J.D. Holliday, C. O'Dowd, and P. Willett Effectiveness of 2D fingerprints for scaffold hopping Future Medicinal Chemistry 3 2011 405 414
10. A. Badel, J.P. Mornon, and S. Hazout Searching for geometric molecular shape complementarity using bidimensional surface profiles Journal of Molecular Graphics 10 1992 205 211
11. B.K. Shoichet, and I.D. Kuntz Matching chemistry and shape in molecular docking Protein Engineering 6 1993 723 732
12. M. Rosen, S.L. Lin, H. Wolfson, and R. Nussinov Molecular shape comparisons in searches for active sites and functional similarity Protein Engineering 11 1998 263 277
13. R. Norel, H.J. Wolfson, and R. Nussinov Small molecule recognition: solid angles surface representation and molecular shape complementarity Combinatorial Chemistry and High Throughput Screening 2 1999 223 237
14. D.A. Cosgrove, D.M. Bayada, and A.P. Johnson A novel method of aligning molecules by local surface shape similarity Journal of Computer-Aided Molecular Design 14 2000 573 591
15. T. Kotani, and K. Higashiura Rapid evaluation of molecular shape similarity index using pairwise calculation of the nearest atomic distances Journal of Chemical Information and Computer Science 42 2002 58 63
16. P.K. Agarwal, N.H. Mustafa, and Y. Wang Fast molecular shape matching using contact maps Journal of Computational Biology 14 2007 131 143
17. V. Venkatraman, P.R. Chakravarthy, and D. Kihara Application of 3D Zernike descriptors to shape-based ligand similarity searching Journal of Chemical Information 1 2009 19
18. Y.S. Liu, Y. Fang, and K. Ramani IDSS: deformation invariant signatures for molecular shape comparison BMC Bioinformatics 10 2009 157
19. Y.S. Liu, Q. Li, G.Q. Zheng, K. Ramani, and W. Benjamin Using diffusion distances for flexible molecular shape comparison BMC Bioinformatics 11 2010 480
20. P.J. Ballester, and W.G. Richards Ultrafast shape recognition to search compound databases for similar molecular shapes Journal of Computational Chemistry 28 2007 1711 1723
21. W. Cai, X. Shao, and B. Maigret Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening Journal of Molecular Graphics and Modelling 20 2002 313 328
22. W. Cai, J.W. Xu, X. Shao, and B. Maigret Molecular simulations using spherical harmonics Chinese Journal of Chemistry 21 2003 1252 1255
23. M.E. Yamagishi, N.F. Martins, G. Neshich, W. Cai, X. Shao, A. Beautrait, and B. Maigret A fast surface-matching procedure for protein-ligand docking Journal of Molecular Modeling 12 2006 965 972
24. W. Cai, J. Xu, X. Shao, V. Leroux, A. Beautrait, and B. Maigret SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces Journal of Molecular Modeling 14 2008 393 401
25. A. Beautrait, V. Leroux, M. Chavent, L. Ghemtio, M.D. Devignes, M. Smail-Tabbone, W. Cai, X. Shao, G. Moreau, P. Bladon, J. Yao, and B. Maigret Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment Journal of Molecular Modeling 14 2008 135 148
26. R.J. Morris, R.J. Najmanovich, A. Kahraman, and J.M. Thornton Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons Bioinformatics 21 2005 2347 2355
27. D.W. Ritchie, and G.J.L. Kemp Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces Journal of Computational Chemistry 20 1999 383 395
28. W. Cai, M. Zhang, and B. Maigret New approach for representation of molecular surface Journal of Computational Chemistry 19 1998 1805 1815
29. A.Y. Meyer, and W.G. Richards Similarity of molecular shape Journal of Computer-Aided Molecular Design 5 1991 427 439
30. G.W. Bemis, and I.D. Kuntz A fast and efficient method for 2D and 3D molecular shape description Journal of Computer-Aided Molecular Design 6 1992 607 628
31. B.S. Duncan, and A.J. Olson Shape analysis of molecular surfaces Biopolymers 33 1993 231 238
32. A.C. Good, T.J. Ewing, D.A. Gschwend, and I.D. Kuntz New molecular shape descriptors: application in database screening Journal of Computer-Aided Molecular Design 9 1995 1 12
33. J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar, and S. Subramaniam Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape Proteins: Structure Function and Bioinformation 33 1998 1 17
34. M. Randic Novel shape descriptors for molecular graphs Journal of Chemical Information and Computer Science 41 2001 607 613
35. F. Weinhold Chemistry. A new twist on molecular shape Nature 411 2001 539 541
36. M.L. Mansfield, D.G. Covell, and R.L. Jernigan A new class of molecular shape descriptors. 1. Theory and properties Journal of Chemical Information and Computer Science 42 2002 259 273
37. W.H. Sauer, and M.K. Schwarz Molecular shape diversity of combinatorial libraries: a prerequisite for broad bioactivity Journal of Chemical Information and Computer Science 43 2003 987 1003
38. F. Fontaine, M. Pastor, and F. Sanz Incorporating molecular shape into the alignment-free grid-independent descriptors Journal of Medicinal Chemistry 47 2004 2805 2815
39. Y. Zyrianov Distribution-based descriptors of the molecular shape Journal of Chemical Information and Modeling 45 2005 657 672
40. S. Putta, and P. Beroza Shapes of things: computer modeling of molecular shape in drug discovery Current Topics in Medicinal Chemistry 7 2007 1514 1524
41. L. Mavridis, B.D. Hudson, and D.W. Ritchie Toward high throughput 3D virtual screening using spherical harmonic surface representations Journal of Chemical Information and Modeling 47 2007 1787 1796
42. V.I. Perez-Nueno, D.W. Ritchie, J.I. Borrell, and J. Teixido Clustering and classifying diverse HIV entry inhibitors using a novel consensus shape-based virtual screening approach: further evidence for multiple binding sites within the CCR5 extracellular pocket Journal of Chemical Information and Modeling 48 2008 2146 2165
43. V.I. Perez-Nueno, D.W. Ritchie, O. Rabal, R. Pascual, J.I. Borrell, and J. Teixido Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking Journal of Chemical Information and Modeling 48 2008 509 533
44. J.A. Wilson, A. Bender, T. Kaya, and P.A. Clemons Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors Journal of Chemical Information and Modeling 49 2009 2231 2241
45. S. Kortagere, M.D. Krasowski, and S. Ekins The importance of discerning shape in molecular pharmacology Trends in Pharmacological Sciences 30 2009 138 147
46. A. Nicholls, G.B. McGaughey, R.P. Sheridan, A.C. Good, G. Warren, M. Mathieu, S.W. Muchmore, S.P. Brown, J.A. Grant, J.A. Haigh, N. Nevins, A.N. Jain, and B. Kelley Molecular shape and medicinal chemistry: a perspective Journal of Medicinal Chemistry 53 2010 3862 3886
47. J.O. Ebalunode, and W. Zheng Molecular shape technologies in drug discovery: methods and applications Current Topics in Medicinal Chemistry 10 2010 669 679
48. P.J. Ballester, I. Westwood, N. Laurieri, E. Sim, and W.G. Richards Prospective virtual screening with ultrafast shape recognition: the identification of novel inhibitors of arylamine N-acetyltransferases Journal of the Royal Society, Interface 7 2009 335 342
49. H. Li, J. Huang, L. Chen, X. Liu, T. Chen, J. Zhu, W. Lu, X. Shen, J. Li, R. Hilgenfeld, and H. Jiang Identification of novel falcipain-2 inhibitors as potential antimalarial agents through structure-based virtual screening Journal of Medicinal Chemistry 52 2009 4936 4940
50. S.W. Muchmore, A.J. Souers, and I. Akritopoulou-Zanze The use of three-dimensional shape and electrostatic similarity searching in the identification of a melanin-concentrating hormone receptor 1 antagonist Chemical Biology and Drug Design 67 2006 174 176
51. E. Naylor, A. Arredouani, S.R. Vasudevan, A.M. Lewis, R. Parkesh, A. Mizote, D. Rosen, J.M. Thomas, M. Izumi, A. Ganesan, A. Galione, and G.C. Churchill Identification of a chemical probe for NAADP by virtual screening Nature Chemical Biology 5 2009 220 226
52. J.A. Grant, M.A. Gallardo, and B.T. Pickup A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape Journal of Computational Chemistry 17 1996 1653 1666
53. A. Nicholls, and J.A. Grant Molecular shape and electrostatics in the encoding of relevant chemical information Journal of Computer-Aided Molecular Design 19 2005 661 686
54. A. Jennings, and M. Tennant Selection of molecules based on shape and electrostatic similarity: proof of concept of "electroforms" Journal of Chemical Information and Modeling 47 2007 1829 1838
55. M.J. Vainio, J.S. Puranen, and M.S. Johnson ShaEP: molecular overlay based on shape and electrostatic potential Journal of Chemical Information and Modeling 49 2009 492 502
56. M.S. Armstrong, G.M. Morris, P.W. Finn, R. Sharma, L. Moretti, R.I. Cooper, and W.G. Richards ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics Journal of Computer-Aided Molecular Design 24 2010 789 801
57. N. Huang, B.K. Shoichet, and J.J. Irwin Benchmarking sets for molecular docking Journal of Medicinal Chemistry 49 2006 6789 6801
58. Standardizer, JChem version 5.4, 2011, Chemaxon, Budapest, Hungary.
59. Pmapper, JChem version 5.4, 2011, Chemaxon, Budapest, Hungary.
60. J. Kirchmair, P. Markt, S. Distinto, G. Wolber, and T. Langer Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-what can we learn from earlier mistakes? Journal of Computer-Aided Molecular Design 22 2008 213 228
61. J.F. Truchon, and C.I. Bayly Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem Journal of Chemical Information and Modeling 47 2007 488 508
62. W. Zhao, K.E. Hevener, S.W. White, R.E. Lee, and J.M. Boyett A statistical framework to evaluate virtual screening BMC Bioinformatics 10 2009 225
63. R.P. Sheridan Alternative global goodness metrics and sensitivity analysis: heuristics to check the robustness of conclusions from studies comparing virtual screening methods Journal of Chemical Information and Modeling 48 2008 426 433
64. S.J. Swamidass, C.A. Azencott, K. Daily, and P. Baldi A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval Bioinformatics 26 2010 1348 1356
65. J.A. Hanley, and B.J. McNeil The meaning and use of the area under a receiver operating characteristic (ROC) curve Radiology 143 1982 29 36
66. V. Venkatraman, V.I. Perez-Nueno, L. Mavridis, and D.W. Ritchie Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods Journal of Chemical Information and Modeling 50 2010 2079 2093
67. T. Fawcett An introduction to ROC analysis Pattern Recognition Letters 27 2006 861 874
68. P.C. Hawkins, G.L. Warren, A.G. Skillman, and A. Nicholls How to do an evaluation: pitfalls and traps Journal of Computer-Aided Molecular Design 22 2008 179 190
69. M.D. Mackey, and J.L. Melville Better than random? The chemotype enrichment problem Journal of Chemical Information and Modeling 49 2009 1154 1162
70. F.J. Provost, T. Fawcett, and R. Kohavi The case against accuracy estimation for comparing induction algorithms J.W. Shavlik, Proceedings of the Fifteenth International Conference on Machine Learning 1998 Morgan Kaufmann Publishers Inc. Madison, Wisconsin, USA 445 453
71. D. Giganti, H. Guillemain, J.L. Spadoni, M. Nilges, J.F. Zagury, and M. Montes Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment Journal of Chemical Information and Modeling 50 2010 992 1004
72. J. Kirchmair, S. Distinto, P. Markt, D. Schuster, G.M. Spitzer, K.R. Liedl, and G. Wolber How to optimize shape-based virtual screening: choosing the right query and including chemical information Journal of Chemical Information and Modeling 49 2009 678 692
73. V.I. Perez-Nueno, and D.W. Ritchie Using consensus-shape clustering to identify promiscuous ligands and protein targets and to choose the right query for shape-based virtual screening Journal of Chemical Information and Modeling 51 2011 1233 1248